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Long-term ecological research has become a cornerstone of the scientific endeavour to better understand ecosystem responses to environmental change. This paper provides a perspective on how such research could be advanced. It emphasizes that a profound understanding of the mechanisms underlying these responses requires that records of ecologic processes be not only sufficiently long, but also collected at an appropriate temporal resolution. We base our argument on an overview of studies of climate impacts in limnic and marine ecosystems, suggesting that lakes and oceans respond to (short-term) weather conditions during critical time windows in the year. The observed response patterns are often time-lagged or driven by the crossing of thresholds in weather-related variables (such as water temperature and thermal stratification intensity). It becomes clear from the previous studies that average annual, seasonal or monthly climate data often fall short of characterizing the thermal dynamics that most organisms respond to. To illustrate such literature-based evidence using a concrete example, we compare 2 years of water temperature data from Müggelsee (Berlin, Germany) at multiple temporal scales (from hours to years). This comparison underlines the pitfalls of analysing data at resolutions not high enough to detect critical differences in environmental forcing. Current science initiatives that aim at improving the temporal resolution of long-term observatory data in aquatic systems will help to identify adequate timescales of analysis necessary for the understanding of ecosystem responses to climate change.